The Old Church
by hellomynameisphoebe
Summary: When Clary was young, her mother gave her up to protect her and she was adopted into a human family. She begins to train to be a Shadowhunter with the Lightwoods, while she must still act normal for her adoptive family. JxC
1. Chapter 1

**Hi! This story has been adopted from Hannah Lightwood, so thank her for the fantastic first chapter, the brilliant ideas and the creation of some of the characters! Also, thanks for letting me adopt the story and helping me keep it true to your idea :)**

**And many of the characters, setting and ideas belong to Cassandra Clare, not me :(**

**Anyone who has already read the story (of the same name) by Hannah Lightwood, this chapter will seem familiar as it is the same as hers to save you guys having to do that annoying flick between stories!**

**The next chapter which was written by me will be posted sooonn, so be patient and tell me what you think!**

"Beep..beep..beep," Emily's alarm clock rang, getting faster with every beep she didn't shut it off. Emily slapped her hand around the remote and gave a too harsh push on the sleep button to turn it off. _God, it sounds like the death alarm,_ Emily thought, shivers running down her spine. She shut her eyes giving her one more second of peacefulness before hulling herself out of her toasty bed. _How come you're always tired after the alarm goes off? _She thought to herself, rubbing her eyes and stretching some more_. I should go get Clary up before Mom yells at her. No one wants her screeching this early in the morning._Emily, with a huff, willed her body to move and put on a pair slippers then, glided over to her sister's bedroom, on the other side of the hall. She knocked on her door before entering, "Clary? Clary, it's time to get up." Emily called to her sister.

Emily slid her eyes over the room. It was like a monk lived there or something, everything was in a specific place and nice neat orders. _It's like no one lives in the here_, Emily thought to herself, _if she spent this much effort in her school work, she might actually be a good student. _Emily chuckled to herself_, Clary a good student? That's priceless. _Emily laughed at the thought but promptly stopped when she saw something from the corner of her eye, Clary was sneaking through the window. Her dark hair was pulled up in a tight bun with a ruby-studded dagger sticking through it. Clary's lanky body was drenched in all black clothing fitting her _very_ tightly in places their mother would _not_ approve of. Through her belt she had some sort of a long blade thing and it was dimly glowing.

The image of her sister shocked Emily stiff, she has never been more terrified of one person in her life and it was her sister; the same innocent child their parents adopted when Emily was 2 and her best friend. Clary, not yet aware of her sister's presence, finished slithering her way through the window, as smoothly as a snake would. Clary then glanced around her room and stopped, noticing Emily standing in the room. Clary tried to keep the shock out of her voice by replacing it with anger at her sister for being in her room, "What the hell are you doing in my room?" She tried to put as much venom in her voice as possible.

Emily was suddenly filled with anger at her sister, "What am _I _doing? You're the one sneaking into the house at 5 o'clock in the morning, on a school day, wearing God knows what. Plus, you have a dagger in your hair and a knife, that looks like in belongs in a _Saw_ movie through your belt!" Emily exclaimed to her sister, "Wait 'till Mom and Dad find out. You're dead." Clary faltered, she couldn't let Emily tell Mom and Dad, she's been enough trouble this week alone.

"No! Emily you can't! If you they'll put me on house arrest. Then I can't go and hu-" Clary cut off immediately, terrified at was she was just about to tell her sister.

"Can't do what? And with who?" Emily asked

"Nothing you'd be interested in and no one you know." Clary responded, very tersely. _Oh no! Why'd I say that? She in definitely not going to get off the subject now_, Clary thought, thinking of ways to stop her sister from asking anymore questions.

"Clary what is going on?" Emily said, desperation thick in her voice, "Please, just tell me you know you can, you've always told me everything. I won't tell Mom and Dad if you just tell me yourself."

"I can't, Emily." Clary spoke, her voice vibrating with despair.

"Why not? Like I've said, you've always told me-" She was cut off by a now very annoyed Clary, "It's not like that this time Emily."


	2. Chapter 2

**Here is chapter 2, written by me :) and from here on, its all me. I should be able to do some more chapters soon... This basically continues on from the last chapter :)**

"Then what's it like, Clare?" Emily's voice was a mixture of annoyance and desperation. "I tell you everything. Stuff I'm afraid to tell mum and even dad, I would trust you with my life. I thought you felt the same."

Emily stood, still in the doorway of the room. It was 5 am in the morning, and the early start, coupled with the shock and sadness had seemed to have drawn the brightness from her normally happy and alive figure. Where normally, her back stood straight, her shoulders back with an air of pride and confidence, instead stood a what could be called a sack of potatoes. Her shoulders were slumped forward in a cower, her back carelessly bent in a way that would put their refined and modest mother to shame. The ringlet curls of her hair, her most defining feature, had even departed leaving a tangled mess of frizz.

"I do, Em," Clary nodded slightly, the gesture accounting for more than her words. Her voice had changed into something more compassionate, but behind it you could still taste the venom that had seemed to seep through her word recently. "It's bigger than that, than life and death. This time, it's not just me."

Emily had never known her sister to move so fast, it seemed that she had blinked, a momentary lapse in her concentration, an error of timing and the door stood mere centimetres from her straight nose.

Her eyes were wide, in a sort of trance, the trauma of what she had seen sent her mind buzzing in infinite circles, destined to never slow.

_Why did Clary have blades? Was she a killer? No, that cant be right, Clary wouldn't hurt a fly. Maybe she had joined a form of martial arts? Something Japanese maybe, like Katana or Kendo. Maybe she thought I'd dob her into mum... What is she joined a cult? Or was recruited into the CIA?_

* * *

><p>Clary sat on the crisply folded, stark white sheets of her bed. They were like the rest of her room- plain, orderly and completely unlike her. Here, in this house with the people she had grown up knowing as Mum, Dad and her sister Emily lived a different Clary. It was an escape from the world of Shadowhunters, of secrets and mysteries and the plain white provided her with a sense of calm and tranquility that the paint-splattered, drawing littered room of the Institute failed to provide. That Clary was more alive than this one, she had a purpose, a real name, parents that were really hers and the Lightwoods.<p>

In the old, rundown church that people saw superficially, was her life. It had taken a change encounter- something that ran deeper than luck. Maybe it was fate, or even just instinct but she had found them. Jace, Isabella and Alec were her family but although she loved her family here, with Mum, Dad and Emily she wasn't truly herself. It was too big a secret. There were so many things they couldn't know; both for her sake, and for theirs.

She wondered what Emily would think of her now. Would she listen if she told her? Would she trust the words that came out of her mouth or would she close her mind off to what seems logical. But, she guessed, no-one would take all to kindly to being told that their were monsters in this world, that lurked in corners preying on the innocent.

It was nearing dawn, and soon Clarys mother would stomp down the hallway, making a racket. She would slowly open the door to Clary's spotless room, only to see the bed seemingly unslept in and presume that Clary had merely left early. She would never guess that after CLary had shut the door in Emily's face, she had packed the essentials- a change of clothes, a toothbrush and the long, awkward length, pencil like object that Clary kept by her side always- and climbed out the window the way she had come in not thirty minutes before.

She planned to return this place that had been her home for almost fourteen years. James and Elizabeth- her classical, adoptive parents had taken over the job of raising her how they thought she should be. But she wasn't like them. Clary wasn't normal, nor was she normal for what she was. Clary had discovered secrets during her search for biological parents that had scared her at first.

With a thud, she landed on the soft, worn ground that had become her portal from one world to another.

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